[Bioperl-l] PHYLIP problem.

[#Raul#~~ WeAtHerEd~~]

Dear sir,

I installed PHYLIP locally and ran the input file on it and the output was
given in a  flash. This seems to be the miss of a package that has to be
installed since it isn't working on my friend's computer too. I haven't
tried the program on windows. I tried changing the folder of my input file
and running the program but it still refuses to work. I will try working out
the rest of the function availavle in the documentation and let you know if
I am getting any further errors after skipping the protdist function.

Thank you,
Rahul
On Thu, Jul 17, 2008 at 4:57 PM, Dave Messina <David.Messina at sbc.su.se>
wrote:

> Hi Rahul,
> Please keep the mailing list on the Cc so that this discussion can be
> archived and others can see it.
>
> There's an error in your program -- you change the variable for the input
> file from $inputfilename in one place to $inputfile in another. It's a
> good idea to always use warnings and use strict with Perl. With warnings,
> the first error shown is:
>
> Name "main::inputfile" used only once: possible typo at test.pl line 9.
>
> which indicates that there is something wrong with $inputfile.
>
> Here's the complete program I ran:
> #!/usr/bin/perl
>
>
> use warnings;
> use strict;
> use Bio::Tools::Run::Phylo::Phylip::ProtDist;
>
> my $inputfilename = 'align.phy';
> my $prodistfactory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new();
>
> my ($matrix)= $prodistfactory->run($inputfilename);
> print $matrix->print_matrix;
>
>
> Note that your perl may be in a different location than mine, so the first
> line may need to be changed. Also note that I changed the location of the
> input file -- it was in the same directory as my Perl script.
>
> The error you saw about 'protdist did not create matrix correctly' is
> unfortunately vague. It simply means that, for some reason, protdist didn't
> produce any output that BioPerl could see. A likely reason for this to occur
> is that protdist didn't run at all.
>
> Have you installed PHYLIP (and specifically protdist), and have you tried
> running it outside of BioPerl?
>
>
> Dave
>
>
>
> On Thu, Jul 17, 2008 at 16:34, #Raul#~~ WeAtHerEd~~ <
> potterbond007 at gmail.com> wrote:
>
>> Dear Dave,
>>
>> I added the print line and the error message that I used to receive
>> changed but the program is still refusing to run.
>>
>> Modified program
>>
>> use Bio::Tools::Run::Phylo::Phylip::ProtDist;
>>
>> my $inputfilename = '/home/rc174/pro/align.phy';
>> #@params = ('MODEL' => 'PAM');
>> my $prodistfactory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new();
>> my ($matrix)= $prodistfactory->run($inputfile);
>>  print $matrix->print_matrix;
>>
>>
>>  The error I receive is now
>>
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: Problems setting up for protdist. Probably bad input data in  !
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:328
>> STACK: Bio::Tools::Run::Phylo::Phylip::ProtDist::run
>> /usr/local/share/perl/5.8.8/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm:362
>> STACK: phylip2.pl:6
>>
>> The error I used to receive before I inserted the line was,
>>
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: protdist did not create matrix correctly (/tmp/S3a5QG6CCd/outfile)
>> STACK: Error::throw
>> STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:328
>> STACK: Bio::Tools::Run::Phylo::Phylip::ProtDist::_run
>> /usr/local/share/perl/5.8.8/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm:409
>> STACK: Bio::Tools::Run::Phylo::Phylip::ProtDist::run
>> /usr/local/share/perl/5.8.8/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm:366
>> STACK: phylip.pl:55
>> -----------------------------------------------------------
>>
>> Is this because I have missed out any specific packages for installation.
>> I use an Ubuntu Linux computer version 7.10 . I am not sure of the bioperl
>> version. I am trying to learn a bit of bioperl on my own so if you could
>> send me a model program for getting a tree so that I could work out the
>> issues I am facing I would be grateful.
>>
>> Cheers,
>> Rahul
>>
>